How rapidly can the major functional components of a soil ecosystem appear in volcanic ash?
The overall conclusion from comparing the functional composition of the developing ash-soil with natural forest soils from the same climates, is that the major biological aspects of the system have developed surprisingly quickly. Already by the 24-month and 36-month stage, the ash-soil had a similar diversity of bacterial functional genes to a forest soil (Fig. 8).
This contrasts with the findings of Fujimura et al.3, who found that ash deposited by the Miyakejima volcano still showed a very distinct and low diversity community compared to that expected of normal forest soils. This difference could be attributable to differences in the initial chemical composition of the ash: the pH value of the Miyakejima ash studied by Fujimura et al.3 was much lower than the ash we sampled, due to the persistence of acids from the initial eruption, or acidic rainfall from later outgassing. Our Sakurajima ash samples had only a slightly acidic pH (5.2) at the time of harvesting, which was similar to the average value (5.14) of 251 ash samples from Sakarajima collected from 1955 to 200125, and they remained in the 5–6 pH range at both 24 months and 36 months. Even the ash soil mesocosm samples that were situated on the lower slopes of the Sakurajima volcano, and the nearby natural forest soils at Sakurajima, remained in the pH 5–6 range and had a similar gene composition to other sites, suggesting that the area around the Sakurajima volcano is not subject to frequent highly acidic rain events. The difference between the Sakurajima ash and the Miyakejima ash hints at the importance of details of the chemical environment of the ash for determining its development into a functioning soil ecosystem.
Another factor which may explain the difference between the paths of biota development of the ash from the two volcanoes is the relative availability of propagules. Our ash soils were surrounded by developed ecosystems which could provide a rain of propagules of microorganisms and bryophytes in windblown dust or in rain splash. By contrast the Miyakejima ash field was an area of extensive ecosystem destruction. If bryophytes and lichens had not been able to establish due to unavailability of propagules, an important source of photosynthetically-fixed energy would have been unavailable to the Miyakejima system. This would have impeded the development of a decomposer food chain, of mineral weathering by organic acids and chelates, and of buffering of soil pH and water content and nutrient storage on organic matter and clay surfaces.
Was there a lower taxonomic diversity than is normally found in a developed soil?
At the broadest level, from the metagenomes, the taxonomic composition of the biota of the developing ash-soil resembled that of the developed forest soils—with archaea, fungi, protists and metazoans occurring at similar relative abundances in the ash-soils and forest soils. In this sense, the ash-soil had developed remarkably quickly in terms of the basic taxonomic framework of a functioning soil ecosystem. Bryophytes and lichens were able to establish10,26 with their propagules small enough to enter through the gauze covering, and presumably played an important role in providing carbon and extra niches to the developing ecosystem—even though they are unlikely to be as supportive of a diverse soil biota as the extensive root systems of vascular plants.
There was however—continuing a pattern seen in the 24-month results reported by Kerfahi et al.10—a lower OTU and Shannon diversity of bacteria based on the 16S rRNA amplicon sequencing. The continuing lower OTU-level 16S taxonomic diversity of the ash soils might have had multiple causes.
Firstly, limitations on dispersal and colonization of the ash soil systems might have kept OTU diversity lower. It is assumed that the biota present were mostly derived from the surrounding forest ecosystems—as windblown or rain splashed material. Dispersal limitation of soil biota is likely to play some role in all volcanic ash fields, although the existence of nearby areas of surviving ecosystem is also common20,27. Most volcanic explosions or ash fields result in no more than a few square kilometres of landscape being completely devastated, and isolated pockets of vegetation that survive are common27,28—in this respect the proximity of our mesocosms to natural vegetation may be fairly realistic. In natural ash deposits, upwards colonization by soil biota from buried ‘legacy soils’ is also possible20. In our experiment, upwards colonization from soil below the pots was not possible, and the plastic gauze covering may have prevented access by insects, birds or seeds that could have brought incidental soil biota. It is thus difficult to know for sure whether the overall role of dispersal limitation in our mesocosm systems is stronger or weaker than would generally be the case in natural ash fields. Since natural ash fields themselves are also very heterogenous in terms of area, depth and degree of devastation of natural vegetation, it is especially hard to generalise.
Secondly, the relatively extreme chemical and physical conditions of the volcanic ash itself are also likely play a major role in limiting the bacterial taxonomic diversity of the ash-soil biota in the mesocosms. Although the pH of the ash in our mesocosm systems was not extreme, it may be expected to be droughty due to low organic matter content, and low in available nutrients and organic matter that could sustain soil food chains. Even by 36 months, the organic carbon of the ash-soil was still orders of magnitude lower than in the surrounding forest soils (Supplementary Fig. S1)10,26. Thus, fewer niche types may be viable in the environment of the developing ash.
Nevertheless, although lower level taxonomic diversity of bacteria is clearly lower than in the established forest soils, the metagenome results from the ash soil mesocosms show that most higher level taxonomic groups of bacteria, archaea and eukaryotes are already present by the 24-month and 36-month stage, emphasizing that in some respects the establishment of soil biota has been rapid. While DNA of dead microorganisms blown as dust could have provided the impression of populations being present, it seems unlikely that dead material would be able to disperse in the same relative proportions as in a forest soil, to give a metagenome that resembled a developed soil in all its major groups, in roughly the same relative abundances (Please refer to Fig. 1 in Kerfahi et al.10).
Was there a lower diversity of categories of functional genes of soil biota than are normally found in a developed soil, indicating less functional complexity in the early ash-soil system?
Surprisingly, the richness and diversity of functional gene categories at Level 4 of the SEED Subsystem was not significantly different between the ash mesocosms and the forest soils. Around 97% of the metagenome reads in the ash mesocosms and the forest soil were bacterial, so the much lower OTU diversity of bacteria in the mesocosms would be expected to give a lower functional diversity of genes. The contrast between patterns of taxonomic and functional diversity in the ash mesocosms emphasises the redundancy of gene functions in soil organisms—such that losing a high proportion of taxonomic diversity apparently has no effect on functional diversity. If the level of functional gene diversity is high, this implies that in a general sense the ecosystem can potentially perform a wide variety of functions. Greater functional diversity is also considered to result in greater resilience of the ecosystem29.
We had also hypothesized that the distinct chemical environment of the developing ash would result in increased relative abundance of a number of specific gene categories:
Is there an increased relative abundance of genes (or of prokaryotic genera) associated with autotrophy (e.g. Rubisco gene, coxL gene) in the ash-soils?
We searched for potential taxa and genes which might indicate autotrophic carbon fixation through chemosynthetic oxidation processes. We found a higher relative abundance of Ktedonobacteraceae (Chloroflexi) in the ash soils compared to forest soils, which is a pattern that was also found in previous ash studies21,30. Ktedonobacteraceae is a novel taxonomic group that has only been recently added to the phylogenetic tree of Chloroflexi30,31. Their genome has been reported to be large and they are known to have a wide potential for different metabolic mechanisms32. Ktedonobacteraceae are mostly found in extreme environments, including volcanic ash and hydrothermal vents30.
We had hypothesized that the coxL (carbon monoxide dehydrogenase large chain) gene—which is implicated in autotrophy—would be more abundant in the ash soil samples. Likewise, the rbcL (ribulose bisphosphate carboxylase large chain) gene is involved in carbon fixation and we hypothesized its greater abundance in the ash-soil mesocosms. However, in fact both rbcL and coxL had higher relative abundances in the forest soils.
Although coxL has been mostly linked with chemotrophic organisms living in an extreme environment, due to its potential role for assisting heterotrophic growth in the environments lacking organic matter21,33, it is also one of the more abundant genes in natural forest soils34. Noting that natural forest is one of the largest global sinks of atmospheric CO34,35, the high relative abundance of coxL gene might be due to high abundance of CO in natural forests. Also, the coxL gene might have the potential to participate in other metabolic pathways. The presence of coxL genes in many different types of organisms (e.g. plant symbionts, animal pathogens, etc.) suggests other roles of CO-oxidation by the coxL gene33.
The higher abundance of rbcL in the forest soils in our study might be related to photosynthetic C fixation by cyanobacteria in both the forest soil and ash soils. rbcL gene also have been found in many natural forest sites. By contrast, Fujimura et al.3 found rbcL to be more abundant in developing volcanic ash soils, which might be attributable to differences in the chemical composition of ash or due to details of the mesoocosm system used in our study.
Is there increased relative abundance of genes that are associated with acquisition of nutrients from abiotic sources rather than decomposition of organic matter (e.g. nitrogen fixation genes)?
Contrary to expectations we found no differences in the relative abundance of nitrogen fixation gene (nifH) between the ash soils and forest soils. It is possible that this reflects nitrogen being relatively more limiting in the forest soils, where there is an abundance of organic carbon. It is also possible that in the forest soils, the abundance of labile carbon in the rhizosphere of N-limited plants encourages N fixing bacteria through root secretions36.
Is there increased relative abundance of stress response genes and dormancy related genes?
As hypothesized, we found that dormancy related genes were more abundant in the ash mesocosms than in the forest soils. This would seem to be adaptive in terms of survival of a well-drained ash-soil, low in organic matter, which is apt to dry out. This would depend, however, on the detailed microclimate. Field measurements suggested that in sunny conditions the microclimate in the static air in the trays in which our pots were held was generally around 0.5–1 °C higher than in the open air a meter away, although this difference disappeared in cloudy conditions and at night10. It is possible that our mesocosms (exposed in open sunlight, but covered by a gauze) would have either retained or lost moisture more easily than the soils, and that this might have affected the frequency of drying. We had also anticipated that stress response genes would be more common in the ash mesocosms. However, in this case the stress response category was less common than in the forest soil, surprisingly suggesting that at a cellular level stresses are in fact less common in the ash-soil.
Is there decreased relative abundance of cell–cell interaction related genes?
As anticipated, genes related to cell–cell interactions such as regulation and cell signalling genes and virulence, disease, and defense genes (Fig. 7a,b) were relatively less abundant in the ash mesocosms. This seems to emphasize that complex interactions are less common in the developing ash system than in a fully developed soil with its more abundant and diverse carbon sources. However, bacterial genes found as part of CRISPRs were relatively less abundant in the forests, implying lower intensity of defense mechanisms of bacteria against viruses in the forests compared to ash soils. The relatively low OTU diversity of the ash soils may perhaps allow greater spread and mortality of viruses through populations, necessitating greater investment in defences.
Since Odum37, it has been noted that developing ecosystems tend to be based on tighter and more effective interactions as succession continues. For example, Morriën et al.38 found that during secondary succession of old field ecosystems, co-occurrences of taxa become more predictable and carbon cycling in the decomposer chain more efficient. Empirically our findings seem to agree with the same paradigm, as we found cell–cell interaction genes found to be more abundant in the developed forest soils. It would be very interesting to directly measure decomposer carbon cycling efficiency in ash-soil mesocosm systems as they develop.
Although we focused on 16S rRNA amplicon sequence data for comparing OTU level diversity between samples as taxonomic assignment based on MG-RAST pipeline is very limited39,40, we had briefly compared the family level bacterial community composition assigned based on metagenome sequence data and based on 16S rRNA amplicon sequence data. It is still debatable if whole genome sequencing, which is free from primer bias, is superior in this respect to 16S rRNA amplicon sequencing40. Our data supports the idea that at the bacterial family level, metagenome sequencing covered a larger variety of taxonomic groups than 16S rRNA sequencing.
Source: Ecology - nature.com
